UPDATE: over 3 years later and I still have not fixed this issue, causing a lovely little bass to sit and weep in its case.

Any fresh ideas on what the problem is or how to fix it? Tapping the pickup causes VERY audible noise.... .....also the pickups are completely sealed around the back so I'm assuming I may be SOL regarding repotting the magnets.

Wow. Three years without a single reply.
My suggestion is to check with Lindy Fralin, Seymour Duncan or other professional pickup makers to see if they can ot the pickups for you. In theory, you can do it at home and it would probably help (as per the instructionson Instructables), but in case the coil is broken you'll have to send it someplace for a rewind. If the coil's back is sealed you may well be SOL because if it's epoxy coating, there's no way to open that up without wrecking the coil. Maybe contact a Yamaha dealer to replace them with their own coils?